First off, major kudos to Alex Smith and Vernon Davis for doing it anyway, however think about this scenario instead.
Instead of Alex Smith running 28 yards for a touchdown, he instead runs for 26 and stays in bounds.
New Orleans only has one time out left. So alex gets tackled, and the clock ticks down to the 2 minute warning. The 49ers kneel down or do running plays that don't product a touchdown, with New Orleans calling one time out. The 49ers would kick a field goal on 4th down and then kick the ball back to New Orleans. Depending on how long it took to execute those 3 kneel downs, the Saints would get the ball back with 30 seconds, and no time outs, being forced to kick a field goal to win. I like the 49ers chances in that scenario.
Fortunately for the 49ers the Saints scored very quickly and gave the ball back to SF offense with enough time to complete that winning drive, but it could have been avoided if Alex had done the unthinkable and avoided going into the end zone in the first place.